Not a TL, but I've always been interested in the what if of John of Denmark, the son of Christian II. If he had a lived a few more years he could have contested the election at the death of the usurper Frederick I. As it was OTL the election initially split between Frederick's eldest and thoroughly protestant son, OTL Christian III, and his younger son by his second wife, John of Schleswig-Holstein-Haderslev, who was favored by the Catholics. However the latter was just a teenager. John of Denmark would have only been a few years older but he had a good reputation and more importantly he was half-Habsburg, through is mother Isabella of Austria, so he can get some foreign backing.
I don't know enough about all the players to know how it would work out. Christian II is alive and imprisoned in Denmark, which complicates things and possibly the two Johns just further split the Catholic faction and secure the throne more easily for Christian. But if Christian II would to renounce in favor of his son and the John's brokered a deal whereby John of Denmark becomes King and the other becomes Duke of all of Schleswig-Holstein maybe it could work? Given the shift towards Lutheranism that occurred under Christian III it could be a major POD if it played out differently.